The AAPS Journal

, Volume 6, Issue 3, pp 35–44 | Cite as

Transporter and ion channel gene expression after caco-2 cell differentiation using 2 different microarray technologies

  • Christopher P. Landowski
  • Pascale Anderle
  • Duxin Sun
  • Wolfgang Sadee
  • Gordon L. Amidon


mRNA expression profiles had previously been measured in Caco-2 cells (human colonic carcinoma cells) using either custom-designed spotted oligonucleotide arrays or Affymetrix GeneChip oligonucleotide arrays. The Caco-2 cells used were from different clones and were examined under slightly different culture conditions commonly encountered when Caco-2 cells are used as a model tissue for studying intestinal transport and metabolism in different laboratories. In this study, we compared gene expression profiles of Caco-2 cells generated with different arrays to assess the validity of conclusions derived from the 2 independent studies, with a focus on changes in transporter and ion channel mRNA expression levels on Caco-2 cell differentiation. Significant changes in expression levels upon differentiation were observed with 78 genes, with probes common to both arrays. Of these, 18 genes were upregulated and 36 genes were downregulated. The 2 arrays yielded discrepant results for 24 genes, showing significant changes upon differentiation. The results from the 2 arrays correlated well for genes expressed above average levels (r=0.75,P<0.01, n=25) and poorly for genes expressed at low levels (r=0.08,P>0.05, n=25). Overall correlation across the 2 platforms wasr=0.45 (P<0.01) for the 78 genes, with similar results from both arrays. Despite differences in experimental conditions and array technology, similar results were obtained for most genes.


microarrays Caco-2 cells transporter ion channel platform comparison 


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  1. 1.
    Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome.Science. 2001;291:1304–1351.CrossRefPubMedGoogle Scholar
  2. 2.
    Hughes TR, Marton MJ, Jones AR, et al. Functional discovery via a compendium of expression profiles.Cell. 2000;102:109–126.CrossRefPubMedGoogle Scholar
  3. 3.
    Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays.Nature. 2000;405:827–836.CrossRefPubMedGoogle Scholar
  4. 4.
    Sun D, Lennernas H, Welage LS, et al. Comparison of human duodenum and Caco-2 gene expression profiles for 12,000 gene sequences tags and correlation with permeability of 26 drugs.Pharm Res. 2002;19:1400–1416.CrossRefPubMedGoogle Scholar
  5. 5.
    Chay CH, Cooper CR, Gendernalik JD, et al. A functional thrombin receptor (PAR1) is expressed on bone-derived prostate cancer cell lines.Wrology. 2002;60:760–765.Google Scholar
  6. 6.
    Landowski CP, Sun D, Foster DR, et al. Gene expression in the human intestine and correlation with oral valacyclovir pharmacokinetic parameters.J Pharmacol Exp Ther. 2003;306:778–786.CrossRefPubMedGoogle Scholar
  7. 7.
    Lockhart DJ, Dong H, Byrne MC, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays.Nat Biotechnol. 1996;14:1675–1680.CrossRefPubMedGoogle Scholar
  8. 8.
    Anderle P, Rakhmanova V, Woodford K, Zerangue Z, Sadee W. Messenger RNA expression of transporter and ion channel genes in undifferentiated and differentiated Caco-2 cells compared to human intestine.Pharm Res. 2003;20:3–15.CrossRefPubMedGoogle Scholar
  9. 9.
    Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays.Nucleic Acids Res. 2000;28:4552–4557.CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.Science. 1995;270:467–470.CrossRefPubMedGoogle Scholar
  11. 11.
    Anderle P, Duval M, Draghici S, Kuklin A, Littlejohn TG, Medrano JF, Vilanova D, Roberts MA. Gene expression databases and data mining.Biotechniques. 2003;Mar(suppl):36–44.Google Scholar
  12. 12.
    Ishii M, Hashimoto S, Tsutsumi S, et al. Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis.Genomics. 2000;68:136–143.CrossRefPubMedGoogle Scholar
  13. 13.
    Bittner M. Obtaining and evaluating gene expression profiles with cDNA microarrays. In: Suhai S, ed.Genomics and Proteomics. New York, NY: Kluwer, 2000:5–25.Google Scholar
  14. 14.
    Li J, Pankratz M, Johnson JA. Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays.Toxicol Sci. 2002;69:383–390.CrossRefPubMedGoogle Scholar
  15. 15.
    Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from 2 different microarray technologies.Bioinformatics. 2002;18:405–412.CrossRefPubMedGoogle Scholar
  16. 16.
    Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC. Accuracy and calibration of commercial oligonucleotide and custom cDNA arrays.Nucleic Acids Res. 2002;30:e48.CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Tan PK, Downey TJ, Spitznagel EL, et al. Evaluation of gene expresion measurements from commercial microarray platforms.Nucleic Acids Res. 2003;31:5676–5684.CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Barezak A, Rodriguez MW, Hanspers K, et al. Spotted long oligonucleotide arrays for human gene expression analysis.Genome Res. 2003;13:1775–1785.CrossRefGoogle Scholar
  19. 19.
    Yang MC, Ruan QG, Yang JJ, et al. A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays.Physiol Genomics. 2001;7:45–53.CrossRefPubMedGoogle Scholar
  20. 20.
    Shin HC, Landowski CP, Amidon GL. Transporters in the GI tract. In: Waterbeemd V-d, Lennernäs H, Artursson P, eds.Drug Bioavailability/Estimation of Solubility, Permeability and Absorption. Weinheim Germany: Wiley-VCH; 2003.Google Scholar
  21. 21.
    DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale.Science. 1997;278:680–686.CrossRefPubMedGoogle Scholar
  22. 22.
    Yang YH, Dudoit S, Luu P, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple systematic variation.Nucleic Acids Res. 2002;30:e15.CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Mariadason JM, Corner GA, Augenlicht LH. Genetic reprogramming in pathways of colonic cell maturation induced by short chain fatty acids: comparison with trichostatin a, sulindac, and curcumin and implications for chemoprevention of colon cancer.Cancer Res. 2000;60:4561–4572.PubMedGoogle Scholar
  24. 24.
    Mariadason JM, Arango D, Corner GA, e al. A gene expression profile that defines colon cell maturationin vitro.Cancer Res. 2002;62:4791–4804.PubMedGoogle Scholar
  25. 25.
    Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J. Within the fold: assessing differential expression measures and reproducibility in microarray assays.Genome Biol. 2002, 3(11): research0062.1-0062.12.Google Scholar
  26. 26.
    Pedron T, Thibault C, Sansonetti PJ. The invasive phenotype ofShigella flexneri directs a distinct gene expression pattern in the human intestinal epithelial cell line Caco-2.J Biol Chem. 2003;278:33878–33886.CrossRefPubMedGoogle Scholar
  27. 27.
    Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, Slonim DK. Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls.Genome Biol. 2001;2(12):research0055.Google Scholar
  28. 28.
    Zarrinkar PP, Mainquist JK, Zamora M, et al. Arrays of arrays for highthroughput gene expression profiling.Genome Res. 2001;11:1256–1261.CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Baum M, Bielau S, Rittner N, et al. Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling.Nucleic Acids Res. 2003;31:e151.CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Engle MJ, Goetz GS, Alpers DH. Caco-2 cells express a combination of colonocyte and enterocyte phenotypes.J Cell Physiol. 1998;174:362–369.CrossRefPubMedGoogle Scholar
  31. 31.
    Levy P, Robert A, Picard J. Biosynthesis of glycosaminoglycans in the human colonic tumor cell line Caco-2: structural changes occurring with the morphological differentiation of the cells.Biol Cell. 1988;62:255–264.CrossRefPubMedGoogle Scholar
  32. 32.
    Hidalgo IJ, Raub TJ, Borchardt RT. Characterization of the human colon carcinoma cell line (Caco-2) as a model system for intestinal epithelial permeability.Gastroenterology. 1989;96:736–749.PubMedGoogle Scholar
  33. 33.
    Rothen-Rutishauser B, Braun A, Günthert M, Wunderli-Allenspach H. Formation of multilayers in the Caco-2 cell culture model: a confocal laser scanning microscopy study.Pharm Res. 2000;17:460–465.CrossRefPubMedGoogle Scholar
  34. 34.
    Mariadason JM, Kurt L, Rickard KL, David H, Barkla DH, Augenlicht LH, Gibson PR. Divergent phenotypic patterns and commitment to apoptosis of Caco-2 cells during spontaneous and butyrateinduced differentiation.J Cell Physiol. 2000;183:347–354.CrossRefPubMedGoogle Scholar
  35. 35.
    Fleet JC, Wang L, Vitek O, Craig BA, Edenberg HJ. Gene expression profiling of Caco-2 BBe cells suggests a role for specific signaling pathways during intestinal differentiation.Physiol Genomics. 2003;13:57–68.CrossRefPubMedGoogle Scholar
  36. 36.
    Behrens I, Kissel T. Do cell culture conditions influence the carriermediated transport of peptides in Caco-2 cell monolayers?Eur J Pharm Sci. 2003;19:433–442.CrossRefPubMedGoogle Scholar
  37. 37.
    Bravo SA, Nielsen CU, Amstrup J, Frokjaer S, Brodin B. In-depth evaluation of Gly-Sar transport parameters as a function of culture time in the Caco-2 cell model.Eur J Pharm Sci. 2004;21:77–86.CrossRefPubMedGoogle Scholar
  38. 38.
    Kothapalli R, Yoder SJ, Mane S, Loughran TP Jr. Microarray results: how accurate are they?BMC Bioinformatics. 2002;3:22.CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Geller SC, Gregg JP, Hagerman P, Rocke DM. Transformation and normalization of oligonucleotide microarray data.Bioinformatics. 2003;19:1817–1823.CrossRefPubMedGoogle Scholar
  40. 40.
    Tseng GC, Oh M-K, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.Nucleic Acids Res. 2001;15:2549–2557.CrossRefGoogle Scholar

Copyright information

© American Association of Pharmaceutical Scientists 2004

Authors and Affiliations

  • Christopher P. Landowski
    • 1
  • Pascale Anderle
    • 2
    • 3
  • Duxin Sun
    • 1
  • Wolfgang Sadee
    • 2
    • 3
  • Gordon L. Amidon
    • 1
  1. 1.Department of Pharmaceutical Sciences, College of PharmacyUniversity of MichiganAnn Arbor
  2. 2.Department of Biopharmaceutical Sciences, School of PharmacyUniversity of San FranciscoSan Francisco
  3. 3.Department of Pharmacology, College of Medicine and Public HealthOhio State UniversityColumbus

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